Evolution of circadian genes PER and CRY in subterranean rodents

There is considerable interest in examining how circadian rhythms function and evolve in subterranean rodents that spend its entire life in underground, darkness environments. Here, we investigated the evolution of PER and CRY genes that are important for mammalian biological clocks in the subterranean rodents. We performed phylogenetic analyses using newly sequenced PER and CRY from the subterranean rodent Lasiopodomys mandarinus, the related aboveground rodent Lasiopodomys brandtii, sequences from other rodents available in public databases. The constructed phylogenetic tree revealed no convergence among subterranean rodents. Phylogenetic and selection-pressure analyses revealed the effect of purifying selection (ω < 1) on PER and CRY in subterranean rodents. Additionally, evidence of positive selection on the CRY1 and PER3 genes in several subterranean rodent species suggests adaptations to a dark habitat. Most of the positively selected sites in CRY1 and PER3 were on the C-terminus. Our findings suggest that PER and CRY are highly conserved during evolution as subterranean rodents adapted to the darkness environment, and that the C-terminal domain of CRY1 and PER3 may be the core regulatory structure of circadian rhythms. The study advances our understanding of how major circadian genes evolved in subterranean rodents.